# Fatal error atom C2 not found in buiding block 166MET while combining tdb and rtp **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [December 19, 2024, 3:05pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-buiding-block-166met-while-combining-tdb-and-rtp/10860 "2024-12-19T15:05:49Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![juanjogomez](https://avatars.discourse-cdn.com/v4/letter/j/bcef8e/32.png) [@juanjogomez](https://gromacs.bioexcel.eu/u/juanjogomez)\ **Post date:** [December 19, 2024, 3:05pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-buiding-block-166met-while-combining-tdb-and-rtp/10860/1 "2024-12-19T15:05:49Z")
GROMACS version: gmx, version 2020.1-Ubuntu-2020.1-1 GROMACS modification: Yes/No For the command line: gmx pdb2gmx -f d4\_clean.pdb -o d4\_processed.gro -water spce Select the Force Field: From current directory: 1: CHARMM all-atom force field From ‘/usr/share/gromacs/top’: 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) Where I select the force field 1, charmm36 version jul 2022 The console give me this error: Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff going to rename ./charmm36-jul2022.ff/aminoacids.r2b Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b going to rename ./charmm36-jul2022.ff/carb.r2b Opening force field file ./charmm36-jul2022.ff/carb.r2b going to rename ./charmm36-jul2022.ff/cgenff.r2b Opening force field file ./charmm36-jul2022.ff/cgenff.r2b going to rename ./charmm36-jul2022.ff/ethers.r2b Opening force field file ./charmm36-jul2022.ff/ethers.r2b going to rename ./charmm36-jul2022.ff/lipid.r2b Opening force field file ./charmm36-jul2022.ff/lipid.r2b going to rename ./charmm36-jul2022.ff/metals.r2b Opening force field file ./charmm36-jul2022.ff/metals.r2b going to rename ./charmm36-jul2022.ff/na.r2b Opening force field file ./charmm36-jul2022.ff/na.r2b going to rename ./charmm36-jul2022.ff/silicates.r2b Opening force field file ./charmm36-jul2022.ff/silicates.r2b going to rename ./charmm36-jul2022.ff/solvent.r2b Opening force field file ./charmm36-jul2022.ff/solvent.r2b Reading d4\_clean.pdb… Read ‘’, 1310 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 166 residues with 1310 atoms chain #res #atoms 1 ‘A’ 166 1310 All occupancies are one Opening force field file ./charmm36-jul2022.ff/atomtypes.atp Reading residue database… (Charmm36-jul2022) Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp Opening force field file ./charmm36-jul2022.ff/carb.rtp Opening force field file ./charmm36-jul2022.ff/cgenff.rtp Opening force field file ./charmm36-jul2022.ff/ethers.rtp Opening force field file ./charmm36-jul2022.ff/lipid.rtp Opening force field file ./charmm36-jul2022.ff/metals.rtp Opening force field file ./charmm36-jul2022.ff/na.rtp Opening force field file ./charmm36-jul2022.ff/silicates.rtp Opening force field file ./charmm36-jul2022.ff/solvent.rtp Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb Opening force field file ./charmm36-jul2022.ff/carb.hdb Opening force field file ./charmm36-jul2022.ff/cgenff.hdb Opening force field file ./charmm36-jul2022.ff/ethers.hdb Opening force field file ./charmm36-jul2022.ff/lipid.hdb Opening force field file ./charmm36-jul2022.ff/metals.hdb Opening force field file ./charmm36-jul2022.ff/na.hdb Opening force field file ./charmm36-jul2022.ff/silicates.hdb Opening force field file ./charmm36-jul2022.ff/solvent.hdb Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb Opening force field file ./charmm36-jul2022.ff/carb.n.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb Opening force field file ./charmm36-jul2022.ff/metals.n.tdb Opening force field file ./charmm36-jul2022.ff/na.n.tdb Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb Opening force field file ./charmm36-jul2022.ff/carb.c.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb Opening force field file ./charmm36-jul2022.ff/metals.c.tdb Opening force field file ./charmm36-jul2022.ff/na.c.tdb Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb Back Off! I just backed up topol.top to ./#topol.top.7# Processing chain 1 ‘A’ (1310 atoms, 166 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 254 donors and 238 acceptors were found. There are 356 hydrogen bonds Will use HISE for residue 9 Will use HISE for residue 24 Will use HISE for residue 105 Will use HISE for residue 126 Identified residue LEU1 as a starting terminus. Identified residue MET166 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET6 HIS9 MET19 HIS24 CYS41 MET46 MET51 SD44 NE271 SD146 NE2186 SG322 SD357 SD394 HIS9 NE271 1.034 MET19 SD146 1.580 1.277 HIS24 NE2186 0.390 0.856 1.289 CYS41 SG322 1.867 1.669 0.400 1.599 MET46 SD357 2.032 2.300 1.778 1.744 1.819 MET51 SD394 1.546 0.937 1.350 1.200 1.712 1.808 CYS52 SG401 1.928 1.531 1.894 1.600 2.209 1.734 0.663 CYS60 SG466 2.001 1.720 0.611 1.659 0.574 1.492 1.444 CYS73 SG566 1.916 1.737 0.632 1.581 0.576 1.343 1.475 CYS75 SG586 2.041 1.815 0.539 1.757 0.202 1.808 1.773 MET83 SD650 1.931 1.170 1.192 1.575 1.510 1.995 0.577 CYS87 SG680 2.004 1.685 2.052 1.690 2.358 1.725 0.849 HIS105 NE2827 5.326 5.050 4.905 4.991 5.014 3.858 4.117 MET108 SD844 5.893 5.584 5.447 5.558 5.555 4.441 4.649 MET118 SD926 7.966 7.750 7.714 7.667 7.833 6.531 6.836 HIS126 NE2990 8.126 7.986 7.881 7.831 7.974 6.583 7.074 MET147 SD1156 9.804 9.715 9.456 9.504 9.494 8.090 8.798 MET150 SD1181 10.414 10.311 10.103 10.118 10.154 8.747 9.394 MET165 SD1300 9.213 9.109 8.884 8.913 8.934 7.534 8.192 MET166 SD1308 8.725 8.660 8.501 8.440 8.572 7.104 7.757 CYS52 CYS60 CYS73 CYS75 MET83 CYS87 HIS105 SG401 SG466 SG566 SG586 SD650 SG680 NE2827 CYS60 SG466 1.828 CYS73 SG566 1.837 0.190 CYS75 SG586 2.239 0.483 0.513 MET83 SD650 1.047 1.203 1.305 1.528 CYS87 SG680 0.199 1.968 1.964 2.386 1.242 HIS105 NE2827 3.550 4.444 4.459 4.915 4.130 3.438 MET108 SD844 4.087 4.982 5.006 5.450 4.642 3.979 0.588 MET118 SD926 6.221 7.266 7.271 7.737 6.902 6.083 2.832 HIS126 NE2990 6.459 7.413 7.403 7.875 7.153 6.316 3.058 MET147 SD1156 8.211 8.941 8.924 9.376 8.842 8.075 4.765 MET150 SD1181 8.794 9.597 9.583 10.040 9.446 8.654 5.338 MET165 SD1300 7.599 8.378 8.363 8.820 8.242 7.462 4.151 MET166 SD1308 7.144 8.021 7.997 8.471 7.851 6.996 3.800 MET108 MET118 HIS126 MET147 MET150 MET165 SD844 SD926 NE2990 SD1156 SD1181 SD1300 MET118 SD926 2.351 HIS126 NE2990 2.638 0.730 MET147 SD1156 4.349 2.542 1.978 MET150 SD1181 4.893 2.862 2.396 0.749 MET165 SD1300 3.733 1.930 1.343 0.644 1.221 MET166 SD1308 3.429 1.607 0.915 1.282 1.734 0.746 Linking CYS-41 SG-322 and CYS-75 SG-586… Linking CYS-52 SG-401 and CYS-87 SG-680… Linking CYS-60 SG-466 and CYS-73 SG-566… Start terminus LEU-1: NH3+ End terminus MET-166: MET2 * * * Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1079) Fatal error: atom C2 not found in buiding block 166MET while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) I have to clarify that 166MET is the terminal position of my protein. If anyone has any idea how to fix this error I would appreciate help. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 21, 2024, 2:51am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-buiding-block-166met-while-combining-tdb-and-rtp/10860/2 "2024-12-21T02:51:17Z")
You need to interactively select terminal patching with the `-ter` option, otherwise an incorrect terminus is guessed (quirk of the CHARMM force field and a niche patch that is sometimes used).